details: http://www.bx.psu.edu/hg/galaxy/rev/04a753865407 changeset: 2821:04a753865407 user: Kelly Vincent kpvincent@bx.psu.edu date: Fri Oct 02 10:49:09 2009 -0400 description: Corrected problem with assignment of dbkey to output from BWA and Bowtie tools
2 file(s) affected in this change:
tools/sr_mapping/bowtie_wrapper_code.py tools/sr_mapping/bwa_wrapper_code.py
diffs (39 lines):
diff -r d98b6a559421 -r 04a753865407 tools/sr_mapping/bowtie_wrapper_code.py --- a/tools/sr_mapping/bowtie_wrapper_code.py Fri Oct 02 09:40:49 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper_code.py Fri Oct 02 10:49:09 2009 -0400 @@ -3,13 +3,14 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool): try: refFile = param_dict['refGenomeSource']['indices'].value - dbkey = os.path.split(refFile)[1].split('.')[0] - # deal with the one odd case - if dbkey.find('chrM') >= 0: - dbkey = 'equCab2' - out_data['output'].set_dbkey(dbkey) except: try: refFile = param_dict['refGenomeSource']['ownFile'].dbkey except: - out_data['output'].set_dbkey('?') + out_data['output'].set_dbkey('?') + return + dbkey = os.path.split(refFile)[1].split('.')[0] + # deal with the one odd case + if dbkey.find('chrM') >= 0: + dbkey = 'equCab2' + out_data['output'].set_dbkey(dbkey) diff -r d98b6a559421 -r 04a753865407 tools/sr_mapping/bwa_wrapper_code.py --- a/tools/sr_mapping/bwa_wrapper_code.py Fri Oct 02 09:40:49 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper_code.py Fri Oct 02 10:49:09 2009 -0400 @@ -3,9 +3,10 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool): try: refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value - out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0]) except: try: refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['ownFile'].dbkey except: out_data['output'].set_dbkey('?') + return + out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0])